Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104515
Name   oriT_STEFF_24|unnamed1 in_silico
Organism   Shigella flexneri strain STEFF_24
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055168 (96357..96708 [-], 352 nt)
oriT length   352 nt
IRs (inverted repeats)      255..262, 271..278  (ACCGCTAG..CTAGCGGT)
 192..198, 206..212  (TATAAAA..TTTTATA)
 40..47, 50..57  (GCAAAAAC..GTTTTTGC)
 4..11, 16..23  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 352 nt

>oriT_STEFF_24|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3266 GenBank   WP_000986962
Name   traI_HUZ50_RS23915_STEFF_24|unnamed1 insolico UniProt ID   A0A0K2B7B9
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192018.92 Da        Isoelectric Point: 5.8722

>WP_000986962.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQDETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQIRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(575-626)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   1453 GenBank   WP_001369361
Name   WP_001369361_STEFF_24|unnamed1 insolico UniProt ID   B7LI64
Length   133 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 133 a.a.        Molecular weight: 15409.70 Da        Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(18-61)

TraY domain (TraY)

(72-119)


  Protein structure


Source ID Structure
AlphaFold DB B7LI64

ID   1454 GenBank   WP_001151524
Name   WP_001151524_STEFF_24|unnamed1 insolico UniProt ID   A0A5W2DT22
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14517.48 Da        Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A5W2DT22


T4CP

ID   3195 GenBank   WP_000009324
Name   traD_HUZ50_RS23930_STEFF_24|unnamed1 insolico UniProt ID   _
Length   717 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 717 a.a.        Molecular weight: 81528.14 Da        Isoelectric Point: 5.1126

>WP_000009324.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIILYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEITGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAVYEAWQREQNPDIQQKMQRREEVN
INVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.



ID   3196 GenBank   WP_001064245
Name   traC_HUZ50_RS24020_STEFF_24|unnamed1 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99159.81 Da        Isoelectric Point: 5.8486

>WP_001064245.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 69570..97279

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HUZ50_RS23920 (HUZ50_23755) 68936..69163 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
HUZ50_RS23925 (HUZ50_23760) 69163..69561 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
HUZ50_RS23930 (HUZ50_23765) 69570..71723 - 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
HUZ50_RS23935 (HUZ50_23770) 71976..72707 - 732 WP_023565183 conjugal transfer complement resistance protein TraT -
HUZ50_RS23940 (HUZ50_23775) 72739..73236 - 498 WP_000605857 entry exclusion protein -
HUZ50_RS23945 (HUZ50_23780) 73252..76074 - 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
HUZ50_RS23950 (HUZ50_23785) 76071..77444 - 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
HUZ50_RS23955 (HUZ50_23790) 77444..77824 - 381 WP_001389370 F-type conjugal transfer protein TrbF -
HUZ50_RS23960 (HUZ50_23795) 77811..78152 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HUZ50_RS23965 (HUZ50_23800) 78082..78627 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HUZ50_RS23970 (HUZ50_23805) 78614..78898 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HUZ50_RS23975 (HUZ50_23810) 78979..79293 + 315 WP_001324103 hypothetical protein -
HUZ50_RS23980 (HUZ50_23815) 79295..79642 - 348 WP_001287910 conjugal transfer protein TrbA -
HUZ50_RS23985 (HUZ50_23820) 79658..80401 - 744 WP_001030393 type-F conjugative transfer system pilin assembly protein TraF traF
HUZ50_RS23990 (HUZ50_23825) 80394..80651 - 258 WP_000864318 conjugal transfer protein TrbE -
HUZ50_RS23995 (HUZ50_23830) 80678..82486 - 1809 WP_000821841 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HUZ50_RS24000 (HUZ50_23835) 82483..83121 - 639 WP_000777700 type-F conjugative transfer system pilin assembly protein TrbC trbC
HUZ50_RS24005 (HUZ50_23840) 83130..84122 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
HUZ50_RS24010 (HUZ50_23845) 84119..84751 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HUZ50_RS24015 (HUZ50_23850) 84748..85134 - 387 WP_000099686 type-F conjugative transfer system protein TrbI -
HUZ50_RS24020 (HUZ50_23855) 85131..87758 - 2628 WP_001064245 type IV secretion system protein TraC virb4
HUZ50_RS24025 (HUZ50_23860) 87918..88139 - 222 WP_001278689 conjugal transfer protein TraR -
HUZ50_RS24030 (HUZ50_23865) 88274..88789 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
HUZ50_RS24035 (HUZ50_23870) 88786..89037 - 252 WP_001038342 conjugal transfer protein TrbG -
HUZ50_RS24040 (HUZ50_23875) 89049..89246 - 198 WP_001324648 conjugal transfer protein TrbD -
HUZ50_RS24045 (HUZ50_23880) 89233..89823 - 591 WP_001376242 conjugal transfer pilus-stabilizing protein TraP -
HUZ50_RS24050 (HUZ50_23885) 89813..91240 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HUZ50_RS24055 (HUZ50_23890) 91240..91968 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HUZ50_RS24060 (HUZ50_23895) 91955..92344 - 390 Protein_103 type IV conjugative transfer system protein TraE -
HUZ50_RS24065 (HUZ50_23900) 92438..93666 + 1229 WP_089541817 IS3 family transposase -
HUZ50_RS24070 (HUZ50_23905) 93678..93857 - 180 Protein_105 TraE/TraK family type IV conjugative transfer system protein -
HUZ50_RS24075 (HUZ50_23910) 93879..94190 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HUZ50_RS24080 (HUZ50_23915) 94205..94570 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HUZ50_RS24085 (HUZ50_23920) 94603..94998 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
HUZ50_RS24090 (HUZ50_23925) 95097..95786 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HUZ50_RS24095 (HUZ50_23930) 95973..96356 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HUZ50_RS24100 (HUZ50_23935) 96689..97279 + 591 WP_001376243 transglycosylase SLT domain-containing protein -
HUZ50_RS24105 (HUZ50_23940) 97576..98397 - 822 WP_001234426 DUF932 domain-containing protein -
HUZ50_RS24110 (HUZ50_23945) 98515..98802 - 288 WP_000107535 hypothetical protein -
HUZ50_RS24115 98827..99033 - 207 WP_000547968 hypothetical protein -
HUZ50_RS24120 99103..99275 + 173 Protein_115 hypothetical protein -
HUZ50_RS24125 99273..99503 - 231 WP_071586998 hypothetical protein -
HUZ50_RS24130 (HUZ50_23950) 99723..99848 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HUZ50_RS24135 99790..99939 - 150 Protein_118 plasmid maintenance protein Mok -
HUZ50_RS24140 (HUZ50_23955) 99961..100149 + 189 WP_001299721 hypothetical protein -
HUZ50_RS24145 (HUZ50_23960) 100118..100880 - 763 Protein_120 plasmid SOS inhibition protein A -
HUZ50_RS24150 (HUZ50_23965) 100877..101311 - 435 WP_000845936 conjugation system SOS inhibitor PsiB -
HUZ50_RS24155 (HUZ50_23970) 101366..101563 - 198 Protein_122 hypothetical protein -
HUZ50_RS24160 (HUZ50_23975) 101591..101824 - 234 WP_000005987 DUF905 family protein -

Host bacterium

ID   4954 GenBank   NZ_CP055168
Plasmid name   STEFF_24|unnamed1 Incompatibility group   IncFIB
Plasmid size   125110 bp Coordinate of oriT [Strand]   96357..96708 [-]
Host baterium   Shigella flexneri strain STEFF_24

Cargo genes

Drug resistance gene   aph(3')-Ia, dfrA14, sul2, aph(3'')-Ib, aph(6)-Id, blaCTX-M-15, sitABCD
Virulence gene   iutA, iucC, iucB, iucA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -